@Article{gao2025comparing,
  title = {Comparing step counting algorithms for high-resolution wrist accelerometry data in older adults in the {ARIC} study},
  author = {Sunan Gao and Xinkai Zhou and Lily Koffman and Amal A Wanigatunga and Jennifer A Schrack and Ciprian M Crainiceanu and John Muschelli},
  journal = {The Journals of Gerontology, Series A: Biological Sciences and Medical Sciences},
  pages = {glaf034},
  year = {2025},
  publisher = {Oxford University Press US},
}

@Article{zhao2025objectively,
  title = {Objectively measured physical activity using wrist-worn accelerometers as a predictor of incident {A}lzheimer’s Disease in the {UK} {B}iobank},
  author = {Angela Zhao and Erjia Cui and Andrew Leroux and Xinkai Zhou and John Muschelli and Martin A Lindquist and Ciprian M Crainiceanu},
  journal = {The Journals of Gerontology, Series A: Biological Sciences and Medical Sciences},
  volume = {80},
  number = {2},
  pages = {glae287},
  year = {2025},
  publisher = {Oxford University Press US},
}

@Article{koffman2024evaluating,
  title = {Evaluating Step Counting Algorithms on Subsecond Wrist-Worn Accelerometry: A Comparison Using Publicly Available Data Sets},
  author = {Lily Koffman and John Muschelli},
  journal = {Journal for the Measurement of Physical Behaviour},
  volume = {7},
  number = {1},
  year = {2024},
  publisher = {Human Kinetics},
}

@Article{leroux2024nhanes,
  title = {{NHANES} 2011-2014: Objective physical activity is the strongest predictor of all-cause mortality},
  author = {Andrew Leroux and Erjia Cui and Ekaterina Smirnova and John Muschelli and Jennifer A Schrack and Ciprian M Crainiceanu},
  journal = {Medicine and science in sports and exercise},
  volume = {56},
  number = {10},
  pages = {1926--1934},
  year = {2024},
}

@Article{wright2024open,
  title = {Open Case Studies: Statistics and Data Science Education through Real-World Applications},
  author = {Carrie Wright and Qier Meng and Michael R Breshock and Lyla Atta and Margaret A Taub and Leah R Jager and John Muschelli and Stephanie C Hicks},
  journal = {Journal of Statistics and Data Science Education},
  volume = {32},
  number = {4},
  pages = {331--344},
  year = {2024},
  publisher = {Taylor \& Francis},
}

@Article{zhao2024objectively,
  title = {Objectively measured physical activity using wrist-worn accelerometers as a predictor of incident {A}lzheimer’s Disease in the {UK} {B}iobank},
  author = {Angela Zhao and Erjia Cui and Andrew Leroux and Xinkai Zhou and John Muschelli and Martin A Lindquist and Ciprian M Crainiceanu},
  journal = {The Journals of Gerontology, Series A: Biological Sciences and Medical Sciences},
  pages = {glae287},
  year = {2024},
  publisher = {Oxford University Press US},
}

@Article{savonen2023open,
  title = {Open-source Tools for Training Resources--{OTTR}},
  author = {Candace Savonen and Carrie Wright and Ava M Hoffman and John Muschelli and Katherine Cox and Frederick J Tan and Jeffrey T Leek},
  journal = {Journal of Statistics and Data Science Education},
  volume = {31},
  number = {1},
  pages = {57--65},
  year = {2023},
  publisher = {Taylor \& Francis},
}

@Article{zhao2023modelarray,
  title = {{ModelArray}: An {R} package for statistical analysis of fixel-wise data},
  author = {Chenying Zhao and Tinashe M Tapera and Joëlle Bagautdinova and Josiane Bourque and Sydney Covitz and Raquel E Gur and Ruben C Gur and Bart Larsen and Kahini Mehta and Steven L Meisler and others},
  journal = {Neuroimage},
  volume = {271},
  pages = {120037},
  year = {2023},
  publisher = {Academic Press},
}

@Article{karas2022comparison,
  title = {Comparison of Accelerometry-Based Measures of Physical Activity: Retrospective Observational Data Analysis Study},
  author = {Marta Karas and John Muschelli and Andrew Leroux and Jacek K Urbanek and Amal A Wanigatunga and Jiawei Bai and Ciprian M Crainiceanu and Jennifer A Schrack and others},
  journal = {{JMIR} {mHealth} and {uHealth}},
  volume = {10},
  number = {7},
  pages = {e38077},
  year = {2022},
  publisher = {JMIR Publications Inc., Toronto, Canada},
}

@Article{pham2022ciftitools,
  title = {{ciftiTools}: A package for reading, writing, visualizing, and manipulating {CIFTI} files in {R}},
  author = {Damon D Pham and John Muschelli and Amanda F Mejia},
  journal = {NeuroImage},
  volume = {250},
  pages = {118877},
  year = {2022},
  publisher = {Academic Press},
}

@Article{qi2022genome,
  title = {Genome-wide association studies of 27 accelerometry-derived physical activity measurements identified novel loci and genetic mechanisms},
  author = {Guanghao Qi and Diptavo Dutta and Andrew Leroux and Debashree Ray and John Muschelli and Ciprian Crainiceanu and Nilanjan Chatterjee},
  journal = {Genetic epidemiology},
  volume = {46},
  number = {2},
  pages = {122--138},
  year = {2022},
}

@Article{redd2022curating,
  author = {Andrew D. Redd and Lauren S. Peetluk and Brooke A. Jarrett and Colleen Hanrahan and Sheree Schwartz and Amrita Rao and Andrew E. Jaffe and Austin D. Peer and Carli B. Jones and Chelsea S. Lutz and Clifton D. McKee and Eshan U. Patel and Joseph G. Rosen and Henri Garrison Desany and Heather S. McKay and John Muschelli and Kathleen M. Andersen and Malen A. Link and Nikolas Wada and Prativa Baral and Ruth Young and Denali Boon and M. Kate Grabowski and Emily S. Gurley and {the Novel Coronavirus Research Compendium Team}},
  title = {Curating the Evidence About {COVID-19} for Frontline Public Health and Clinical Care: The Novel Coronavirus Research Compendium},
  journal = {Public Health Reports},
  volume = {137},
  number = {2},
  pages = {197-202},
  year = {2022},
  doi = {10.1177/00333549211058732},
}

@Article{sharrock2022bayesian,
  title = {Bayesian deep learning outperforms clinical trial estimators of intracerebral and intraventricular hemorrhage volume},
  author = {Matthew F Sharrock and W Andrew Mould and Meghan Hildreth and E Paul Ryu and Nathan Walborn and Issam A Awad and Daniel F Hanley and John Muschelli},
  journal = {Journal of Neuroimaging},
  year = {2022},
  volume = {32},
  number = {5},
  pages = {968--976},
}

@Article{smirnova2022predictive,
  title = {Predictive performance of selected breath volatile organic carbon compounds in stage 1 lung cancer},
  author = {Ekaterina Smirnova and Christopher Mallow and John Muschelli and Yuan Shao and Jeffrey Thiboutot and Andres Lam and Ana M Rule and Ciprian Crainiceanu and Lonny Yarmus},
  journal = {Translational Lung Cancer Research},
  volume = {11},
  number = {6},
  pages = {1009},
  year = {2022},
  publisher = {AME Publications},
}

@Article{bennett2021clinical,
  author = {Tellen D. Bennett and Richard A. Moffitt and Janos G. Hajagos and Benjamin Amor and Adit Anand and Mark M. Bissell and Katie Rebecca Bradwell and Carolyn Bremer and James Brian Byrd and Alina Denham and Peter E. DeWitt and Davera Gabriel and Brian T. Garibaldi and Andrew T. Girvin and Justin Guinney and Elaine L. Hill and Stephanie S. Hong and Hunter Jimenez and Ramakanth Kavuluru and Kristin Kostka and Harold P. Lehmann and Eli Levitt and Sandeep K. Mallipattu and Amin Manna and Julie A. McMurry and Michele Morris and John Muschelli and Andrew J. Neumann and Matvey B. Palchuk and Emily R. Pfaff and Zhenglong Qian and Nabeel Qureshi and Seth Russell and Heidi Spratt and Anita Walden and Andrew E. Williams and Jacob T. Wooldridge and Yun Jae Yoo and Xiaohan Tanner Zhang and Richard L. Zhu and Christopher P. Austin and Joel H. Saltz and Ken R. Gersing and Melissa A. Haendel and Christopher G. Chute and National COVID Cohort Collaborative (N3C) Consortium},
  title = {{Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort Collaborative}},
  journal = {JAMA Network Open},
  volume = {4},
  number = {7},
  pages = {e2116901-e2116901},
  year = {2021},
  publisher = {American Medical Association},
  month = {07},
  abstract = {{The National COVID Cohort Collaborative (N3C) is a centralized, harmonized, high-granularity electronic health record repository that is the largest, most representative COVID-19 cohort to date. This multicenter data set can support robust evidence-based development of predictive and diagnostic tools and inform clinical care and policy.To evaluate COVID-19 severity and risk factors over time and assess the use of machine learning to predict clinical severity.In a retrospective cohort study of 1 926 526 US adults with SARS-CoV-2 infection (polymerase chain reaction \\>99\\% or antigen \\<1\\%) and adult patients without SARS-CoV-2 infection who served as controls from 34 medical centers nationwide between January 1, 2020, and December 7, 2020, patients were stratified using a World Health Organization COVID-19 severity scale and demographic characteristics. Differences between groups over time were evaluated using multivariable logistic regression. Random forest and XGBoost models were used to predict severe clinical course (death, discharge to hospice, invasive ventilatory support, or extracorporeal membrane oxygenation).Patient demographic characteristics and COVID-19 severity using the World Health Organization COVID-19 severity scale and differences between groups over time using multivariable logistic regression.The cohort included 174 568 adults who tested positive for SARS-CoV-2 (mean [SD] age, 44.4 [18.6] years; 53.2\\% female) and 1 133 848 adult controls who tested negative for SARS-CoV-2 (mean [SD] age, 49.5 [19.2] years; 57.1\\% female). Of the 174 568 adults with SARS-CoV-2, 32 472 (18.6\\%) were hospitalized, and 6565 (20.2\\%) of those had a severe clinical course (invasive ventilatory support, extracorporeal membrane oxygenation, death, or discharge to hospice). Of the hospitalized patients, mortality was 11.6\\% overall and decreased from 16.4\\% in March to April 2020 to 8.6\\% in September to October 2020 (P = .002 for monthly trend). Using 64 inputs available on the first hospital day, this study predicted a severe clinical course using random forest and XGBoost models (area under the receiver operating curve = 0.87 for both) that were stable over time. The factor most strongly associated with clinical severity was pH; this result was consistent across machine learning methods. In a separate multivariable logistic regression model built for inference, age (odds ratio [OR], 1.03 per year; 95\\% CI, 1.03-1.04), male sex (OR, 1.60; 95\\% CI, 1.51-1.69), liver disease (OR, 1.20; 95\\% CI, 1.08-1.34), dementia (OR, 1.26; 95\\% CI, 1.13-1.41), African American (OR, 1.12; 95\\% CI, 1.05-1.20) and Asian (OR, 1.33; 95\\% CI, 1.12-1.57) race, and obesity (OR, 1.36; 95\\% CI, 1.27-1.46) were independently associated with higher clinical severity.This cohort study found that COVID-19 mortality decreased over time during 2020 and that patient demographic characteristics and comorbidities were associated with higher clinical severity. The machine learning models accurately predicted ultimate clinical severity using commonly collected clinical data from the first 24 hours of a hospital admission.}},
  issn = {2574-3805},
  doi = {10.1001/jamanetworkopen.2021.16901},
  url = {https://doi.org/10.1001/jamanetworkopen.2021.16901},
  eprint = {https://jamanetwork.com/journals/jamanetworkopen/articlepdf/2781923/bennett\_2021\_oi\_210506\_1625605077.56265.pdf},
}

@Article{bowring2021outcome,
  title = {Outcome-stratified analysis of biomarker trajectories for patients infected with severe acute respiratory syndrome Coronavirus 2},
  author = {Mary G Bowring and Zitong Wang and Yizhen Xu and Joshua Betz and John Muschelli and Brian T Garibaldi and Scott L Zeger},
  journal = {American journal of epidemiology},
  volume = {190},
  number = {10},
  pages = {2094--2106},
  year = {2021},
  publisher = {Oxford University Press},
}

@Article{broll2021interpreting,
  title = {Interpreting blood GLUcose data with {R} package {iglu}},
  author = {Steven Broll and Jacek Urbanek and David Buchanan and Elizabeth Chun and John Muschelli and Naresh M Punjabi and Irina Gaynanova},
  journal = {PloS one},
  volume = {16},
  number = {4},
  pages = {e0248560},
  year = {2021},
  publisher = {Public Library of Science San Francisco, CA USA},
}

@Article{garibaldi2021patient,
  title = {Patient trajectories among persons hospitalized for {COVID-19}: a cohort study},
  author = {Brian T Garibaldi and Jacob Fiksel and John Muschelli and Matthew L Robinson and Masoud Rouhizadeh and Jamie Perin and Grant Schumock and Paul Nagy and Josh H Gray and Harsha Malapati and others},
  journal = {Annals of Internal Medicine},
  volume = {174},
  number = {1},
  pages = {33--41},
  year = {2021},
  publisher = {American College of Physicians},
}

@Article{leroux2021quantifying,
  title = {Quantifying the predictive performance of objectively measured physical activity on mortality in the {UK} {Biobank}},
  author = {Andrew Leroux and Shiyao Xu and Prosenjit Kundu and John Muschelli and Ekaterina Smirnova and Nilanjan Chatterjee and Ciprian Crainiceanu},
  journal = {The Journals of Gerontology: Series A},
  volume = {76},
  number = {8},
  pages = {1486--1494},
  year = {2021},
  publisher = {Oxford University Press US},
}

@InProceedings{scully2021sex,
  title = {Sex and gender differences in testing, hospital admission, clinical presentation, and drivers of severe outcomes from {COVID-19}},
  author = {Eileen P Scully and Grant Schumock and Martina Fu and Guido Massaccesi and John Muschelli and Joshua Betz and Eili Y Klein and Natalie E West and Matthew Robinson and Brian T Garibaldi and others},
  booktitle = {Open forum infectious diseases},
  volume = {8},
  number = {9},
  pages = {ofab448},
  year = {2021},
}

@Article{sharrock20213d,
  title = {{3D} deep neural network segmentation of intracerebral hemorrhage: development and validation for clinical trials},
  author = {Matthew F Sharrock and W Andrew Mould and Hasan Ali and Meghan Hildreth and Issam A Awad and Daniel F Hanley and John Muschelli},
  journal = {Neuroinformatics},
  volume = {19},
  number = {3},
  pages = {403--415},
  year = {2021},
  publisher = {Springer US},
}

@Article{torbati2021multi,
  title = {A multi-scanner neuroimaging data harmonization using {RAVEL} and {ComBat}},
  author = {Mahbaneh Eshaghzadeh Torbati and Davneet S Minhas and Ghasan Ahmad and Erin E O’Connor and John Muschelli and Charles M Laymon and Zixi Yang and Ann D Cohen and Howard J Aizenstein and William E Klunk and others},
  journal = {Neuroimage},
  volume = {245},
  pages = {118703},
  year = {2021},
  publisher = {Academic Press},
}

@Article{tustison2021antsx,
  title = {The {ANTsX} ecosystem for quantitative biological and medical imaging},
  author = {Nicholas J Tustison and Philip A Cook and Andrew J Holbrook and Hans J Johnson and John Muschelli and Gabriel A Devenyi and Jeffrey T Duda and Sandhitsu R Das and Nicholas C Cullen and Daniel L Gillen and others},
  journal = {Scientific reports},
  volume = {11},
  number = {1},
  pages = {1--13},
  year = {2021},
  publisher = {Nature Publishing Group},
}

@Article{wang2021moderated,
  title = {Moderated t-tests for group-level {fMRI} analysis},
  author = {Guoqing Wang and John Muschelli and Martin A Lindquist},
  journal = {NeuroImage},
  volume = {237},
  pages = {118141},
  year = {2021},
  publisher = {Academic Press},
}

@Article{wongvibulsin2021development,
  title = {Development of severe {COVID-19} adaptive risk predictor ({SCARP}), a calculator to predict severe disease or death in hospitalized patients with {COVID-19}},
  author = {Shannon Wongvibulsin and Brian T. Garibaldi and Annukka A. R. Antar and Jiyang Wen and Mei-Cheng Wang and Amita Gupta and Robert Bollinger and Yanxun Xu and Kunbo Wang and Joshua F. Betz and John Muschelli and Karen Bandeen-Roche and Scott L. Zeger and Matthew L. Robinson},
  journal = {Annals of internal medicine},
  volume = {174},
  number = {6},
  pages = {777--785},
  year = {2021},
  publisher = {American College of Physicians},
}

@Article{wrobel2021diurnal,
  title = {Diurnal physical activity patterns across ages in a large {UK} based cohort: the {UK} {B}iobank study},
  author = {Julia Wrobel and John Muschelli and Andrew Leroux},
  journal = {Sensors},
  volume = {21},
  number = {4},
  pages = {1545},
  year = {2021},
  publisher = {MDPI},
}

@InProceedings{muschelli2020publicly,
  title = {A Publicly Available, High Resolution, Unbiased {CT} Brain Template},
  author = {John Muschelli},
  booktitle = {International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems},
  pages = {358--366},
  year = {2020},
}

@Article{ding2020improved,
  title = {An improved algorithm of white matter hyperintensity detection in elderly adults},
  author = {T Ding and AD Cohen and EE O’Connor and HT Karim and A Crainiceanu and J Muschelli and O Lopez and WE Klunk and HJ Aizenstein and R Krafty and others},
  journal = {NeuroImage: Clinical},
  volume = {25},
  pages = {102151},
  year = {2020},
  publisher = {Elsevier},
}

@Article{gherman2020rxnat,
  title = {{Rxnat}: an open-source {R} package for {XNAT}-based repositories},
  author = {Adrian Gherman and John Muschelli and Brian Caffo and Ciprian Crainiceanu},
  journal = {Frontiers in {N}euroinformatics},
  volume = {14},
  year = {2020},
  publisher = {Frontiers Media SA},
}

@Article{hannawi2020postcardiac,
  title = {Postcardiac arrest neurological prognostication with quantitative regional cerebral densitometry},
  author = {Yousef Hannawi and John Muschelli and Maximilian Mulder and Matthew Sharrock and Christian Storm and Christoph Leithner and Ciprian M Crainiceanu and Robert D Stevens},
  journal = {Resuscitation},
  year = {2020},
  publisher = {Elsevier},
  volume = {154},
  pages = {101--109},
}

@Article{hansen2020relationship,
  title = {Relationship of White Matter Lesions with Intracerebral Hemorrhage Expansion and Functional Outcome: {MISTIE} {II} and {CLEAR} {III}},
  author = {Björn M Hansen and Natalie Ullman and John Muschelli and Bo Norrving and Rachel Dlugash and Radhika Avadhani and Issam Awad and Mario Zuccarello and Wendy C Ziai and Daniel F Hanley and others},
  journal = {Neurocritical Care},
  pages = {1--9},
  year = {2020},
  doi = {10.1007/s12028-020-00916-4},
  publisher = {Springer},
}

@Article{ari,
  author = {Sean Kross and Jeffrey T. Leek and John Muschelli},
  title = {{ari: The Automated R Instructor}},
  year = {2020},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2020-023},
  url = {https://doi.org/10.32614/RJ-2020-023},
  pages = {258--265},
  volume = {12},
  number = {1},
}

@InProceedings{minhas2020statistical,
  title = {Statistical Methods for Processing Neuroimaging Data from Two Different Sites with a {D}own Syndrome Population Application},
  author = {Davneet S Minhas and Zixi Yang and John Muschelli and Charles M Laymon and Joseph M Mettenburg and Matthew D Zammit and Sterling Johnson and Chester A Mathis and Ann D Cohen and Benjamin L Handen and others},
  booktitle = {International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems},
  pages = {367--379},
  year = {2020},
}

@Article{rothstein2020doctor,
  title = {`{T}he doctor said formula would help me': Health sector influences on use of infant formula in peri-urban {L}ima, {P}eru},
  author = {Jessica D Rothstein and Laura E Caulfield and Elena T Broaddus-Shea and John Muschelli and Robert H Gilman and Peter J Winch},
  journal = {Social Science \& Medicine},
  volume = {244},
  number = {112324},
  year = {2020},
  publisher = {Elsevier},
  doi = {https://doi.org/10.1016/j.socscimed.2019.05.029},
}

@Article{ryan2020template,
  title = {Template Creation for High-Resolution Computed Tomography Scans of the Lung in {R} Software},
  author = {Sarah M Ryan and Brian Vestal and Lisa A Maier and Nichole E Carlson and John Muschelli},
  journal = {Academic radiology},
  volume = {27},
  number = {8},
  pages = {e204--e215},
  year = {2020},
  publisher = {Elsevier},
}

@Article{Valcarcel2020tapas,
  title = {{TAPAS}: A Thresholding Approach for Probability Map Automatic Segmentation in Multiple Sclerosis},
  author = {Alessandra M Valcarcel and John Muschelli and Dzung L Pham and Melissa L Martin and Paul Yushkevich and Rachel Brandstadter and Matthew K Schindler and Kristina R Patterson and Peter A Calabresi and Rohit Bakshi and Russell T Shinohara},
  journal = {NeuroImage: Clinical},
  year = {2020},
  publisher = {Elsevier},
}

@Article{muschelli2019roc,
  author = {John Muschelli},
  title = {{ROC} and {AUC} with a Binary Predictor: a Potentially Misleading Metric},
  journal = {Journal of Classification},
  pages = {1--13},
  year = {2019},
  publisher = {Springer US},
}

@Article{muschelli2019ct,
  author = {John Muschelli},
  title = {Recommendations for Processing Head {CT} Data},
  journal = {Frontiers in Neuroinformatics},
  volume = {13},
  pages = {61},
  year = {2019},
  url = {https://www.frontiersin.org/article/10.3389/fninf.2019.00061},
  doi = {10.3389/fninf.2019.00061},
  issn = {1662-5196},
}

@Article{hadavand2019analysis,
  title = {Analysis of Student Behavior Using the {R} Package {crsra}},
  author = {Aboozar Hadavand and John Muschelli and Jeffrey Leek},
  journal = {Journal of Learning Analytics},
  volume = {6},
  number = {2},
  pages = {140--152},
  year = {2019},
}

@Article{muschelli2018freesurfer,
  title = {{freesurfer}: Connecting the {Freesurfer} software with {R}},
  author = {John Muschelli and Elizabeth Sweeney and Ciprian M Crainiceanu},
  journal = {F1000Research},
  volume = {7},
  year = {2018},
}

@Article{muschelli2017neuroconductor,
  author = {John Muschelli and Adrian Gherman and Jean-Philippe Fortin and Brian Avants and Brandon Whitcher and Jonathan D Clayden and Brian S Caffo and Ciprian M Crainiceanu},
  title = {{Neuroconductor}: an {R} platform for medical imaging analysis},
  journal = {Biostatistics},
  pages = {kxx068},
  year = {2018},
  doi = {10.1093/biostatistics/kxx068},
  url = {+ http://dx.doi.org/10.1093/biostatistics/kxx068},
  eprint = {/oup/backfile/content_public/journal/biostatistics/pap/10.1093_biostatistics_kxx068/1/kxx068.pdf},
}

@Article{commowick2018objective,
  title = {Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure},
  author = {Olivier Commowick and Audrey Istace and Michael Kain and Baptiste Laurent and Florent Leray and Mathieu Simon and Sorina Camarasu Pop and Pascal Girard and Roxana Ameli and Jean-Christophe Ferré and Anne Kerbrat and Thomas Tourdias and Frédéric Cervenansky and Tristan Glatard and Jeremy Beaumont and Senan Doyle and Florence Forbes and Jesse Knight and April Khademi and Amirreza Mahbod and Chunliang Wang and Richard Mckinley and Franca Wagner and John Muschelli and Elizabeth Sweeney and Eloy Roura and Xavier Lladó and Michel M Santos and Wellington P Santos and Abel G Silva-Filho and Xavier Tomas-Fernandez and Hélène Urien and Isabelle Bloch and Sergi Valverde and Mariano Cabezas and Francisco Javier Vera-Olmos and Norberto Malpica and Charles Guttmann and Sandra Vukusic and Gilles Edan and Michel Dojat and Martin Styner and Simon K Warfield and François Cotton and Christian Barillot},
  year = {2018},
  journal = {Scientific Reports},
  volume = {8},
  issue = {1},
  pages = {13650},
}

@Article{smith2018feasibility,
  title = {Feasibility of Coping Effectiveness Training for Caregivers of Children with Autism Spectrum Disorder: a Genetic Counseling Intervention},
  author = {Christy Haakonsen Smith and Erin Turbitt and John Muschelli and Lori Leonard and Katie L Lewis and Brian Freedman and Michelle Muratori and Barbara B Biesecker},
  journal = {Journal of genetic counseling},
  volume = {27},
  number = {1},
  pages = {252--262},
  year = {2018},
  publisher = {Springer US},
}

@InProceedings{valcarcel2018tapas,
  title = {{TAPAS}: threshold adjustment to probability map automatic segmentations},
  author = {AM Valcarcel and J Muschelli and C Crainiceanu and DL Pham and PA Calabresi and R Bakshi and RT Shinohara},
  booktitle = {MULTIPLE SCLEROSIS JOURNAL},
  volume = {24},
  pages = {629--630},
  year = {2018},
}

@Article{valcarcel2018mimosa,
  title = {{MIMoSA}: An Automated Method for Intermodal Segmentation Analysis of Multiple Sclerosis Brain Lesions},
  author = {Alessandra M Valcarcel and Kristin A Linn and Simon N Vandekar and Theodore D Satterthwaite and John Muschelli and Peter A Calabresi and Dzung L Pham and Melissa Lynne Martin and Russell T Shinohara},
  journal = {Journal of Neuroimaging},
  year = {2018},
}

@InProceedings{valcarcel2018mimosa2,
  title = {{MIMoSA}: An Approach to Automatically Segment {T2} Hyperintense and {T1} Hypointense Lesions in Multiple Sclerosis},
  author = {Alessandra M Valcarcel and Kristin A Linn and Fariha Khalid and Simon N Vandekar and Shahamat Tauhid and Theodore D Satterthwaite and John Muschelli and Rohit Bakshi and Russell T Shinohara},
  booktitle = {International MICCAI Brainlesion Workshop},
  pages = {47--56},
  year = {2018},
}

@Article{muschelli2016pitch,
  title = {{PItcHPERFeCT}: Primary Intracranial Hemorrhage Probability Estimation using Random Forests on {CT}},
  journal = {{NeuroImage}: Clinical},
  volume = {14},
  pages = {379 - 390},
  year = {2017},
  issn = {2213-1582},
  doi = {http://dx.doi.org/10.1016/j.nicl.2017.02.007},
  url = {http://www.sciencedirect.com/science/article/pii/S2213158217300414},
  author = {John Muschelli and Elizabeth M. Sweeney and Natalie L. Ullman and Paul Vespa and Daniel F. Hanley and Ciprian M. Crainiceanu},
}

@Article{hanley2017thrombolytic,
  title = {Thrombolytic removal of intraventricular haemorrhage in treatment of severe stroke: results of the randomised, multicentre, multiregion, placebo-controlled {CLEAR} {III} trial},
  author = {Daniel F Hanley and Karen Lane and Nichol McBee and Wendy Ziai and Stanley Tuhrim and Kennedy R Lees and Jesse Dawson and Dheeraj Gandhi and Natalie Ullman and W Andrew Mould and Steven W Mayo and A David Mendelow and Barbara Gregson and Kenneth Butcher and Paul Vespa and David W Wright and Carlos S Kase and J Ricardo Carhuapoma and Penelope M Keyl and Marie Diener-West and John Muschelli and Joshua F Betz and Carol B Thompson and Elizabeth A Sugar and Gayane Yenokyan and Scott Janis and Sayona John and Sagi Harnof and George A Lopez and E Francois Aldrich and Mark R Harrigan and Safdar Ansari and Jack Jallo and Jean-Louis Caron and David LeDoux and Opeolu Adeoye and Mario Zuccarello and Harold P Adams and Michael Rosenblum and Richard E Thompson and Issam A Awad},
  journal = {The Lancet},
  volume = {389},
  number = {10069},
  pages = {603--611},
  year = {2017},
  publisher = {Elsevier},
}

@Article{kickingereder2017radiomic,
  title = {Radiomic subtyping improves disease stratification beyond key molecular, clinical and standard imaging characteristics in patients with glioblastoma.},
  journal = {{Neuro-Oncology}},
  year = {2017},
  author = {Philipp Kickingereder and Ulf Neuberger and David Bonekamp and Paula Piechotta and Michael Götz and Antje Wick and Martin Sill and Annekathrin Kratz and Russell Shinohara and David Jones and Alexander Radbruch and John Muschelli and Andreas Unterberg and Juergen Debus and Heinz-Peter Schlemmer and Christel Herold-Mende and Stefan Pfister and Andreas {von Deimling} and Wolfgang Wick and David Capper and Klaus Maier-Hein and Martin Bendszus},
}

@Article{maier2017isles,
  author = {O. Maier and B.H. Menze and J. {von der Gablentz} and L. Häni and M.P. Heinrich and M. Liebrand and S. Winzeck and A. Basit and P. Bentley and L. Chen and D. Christiaens and F. Dutil and K. Egger and C. Feng and B. Glocker and M. Götz and T. Haeck and H.-L. Halme and M. Havaei and K.M. Iftekharuddin and P.-M. Jodoin and K. Kamnitsas and E. Kellner and A. Korvenoja and H. Larochelle and C. Ledig and J.-H. Lee and F. Maes and Q. Mahmood and K.H. Maier-Hein and R. McKinley and J. Muschelli and C. Pal and L. Pei and J.R. Rangarajan and S.M.S. Reza and D. Robben and D. Rueckert and E. Salli and P. Suetens and C.-W. Wang and M. Wilms and J.S. Kirschke and U.M. Krämer and T.F. Münte and P. Schramm and R. Wiest and H. Handels and M. Reyes},
  title = {{ISLES} 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral {MRI}},
  journal = {Medical Image Analysis},
  year = {2017},
  volume = {35},
  pages = {250-269},
  doi = {10.1016/j.media.2016.07.009},
  note = {cited By 14},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84979950799&doi=10.1016%2fj.media.2016.07.009&partnerID=40&md5=15537a210adbbc102bcef75103bee7df},
  document_type = {Article},
  source = {Scopus},
}

@Article{bundy2016peds,
  title = {Preventive Care Delivery to Young Children With Sickle Cell Disease},
  author = {David G Bundy and John Muschelli and Gwendolyn D Clemens and John J Strouse and Richard E Thompson and James F Casella and Marlene R Miller},
  journal = {Journal of pediatric hematology/oncology},
  volume = {38},
  number = {4},
  pages = {294--300},
  year = {2016},
  publisher = {LWW},
}

@Article{fortin2016removing,
  title = {Removing inter-subject technical variability in magnetic resonance imaging studies},
  author = {Jean-Philippe Fortin and Elizabeth M Sweeney and John Muschelli and Ciprian M Crainiceanu and Russell T Shinohara and Alzheimer's Disease Neuroimaging Initiative and others},
  journal = {NeuroImage},
  volume = {132},
  pages = {198--212},
  year = {2016},
  publisher = {Academic Press},
}

@Article{hanley2016safety,
  title = {Safety and efficacy of minimally invasive surgery plus alteplase in intracerebral haemorrhage evacuation ({MISTIE}): a randomised, controlled, open-label, phase 2 trial},
  author = {Daniel F Hanley and Richard E Thompson and John Muschelli and Michael Rosenblum and Nichol McBee and Karen Lane and Amanda J Bistran-Hall and Steven W Mayo and Penelope Keyl and Dheeraj Gandhi and Tim C Morgan and Natalie Ullman and W Andrew Mould and J Ricardo Carhuapoma and Carlos Kase and Wendy Ziai and Carol B Thompson and Gayane Yenokyan and Emily Huang and William C Broaddus and R Scott Graham and E Francois Aldrich and Robert Dodd and Cristanne Wijman and Jean-Louis Caron and Judy Huang and Paul Camarata and A David Mendelow and Barbara Gregson and Scott Janis and Paul Vespa and Neil Martin and Issam Awad and Mario Zuccarello},
  journal = {The Lancet Neurology},
  volume = {15},
  number = {12},
  pages = {1228--1237},
  year = {2016},
  publisher = {Elsevier},
}

@InProceedings{kickingereder2016large,
  title = {Large-scale radiomic profiling of glioblastoma identifies an imaging signature for predicting and stratifying antiangiogenic treatment response},
  author = {P Kickingereder and M Götz and J Muschelli and A Wick and U Neuberger and R Shinohara and A Radbruch and H Schlemmer and W Wick and M Bendszus and K Maier-Hein and D Bonekamp},
  booktitle = {R{\"o}Fo-Fortschritte auf dem Gebiet der R{\"o}ntgenstrahlen und der bildgebenden Verfahren},
  volume = {188},
  number = {S 01},
  pages = {WISS301\_1},
  year = {2016},
}

@Article{sweeney2016relating,
  title = {Relating multi-sequence longitudinal intensity profiles and clinical covariates in incident multiple sclerosis lesions},
  author = {Elizabeth M Sweeney and Russell T Shinohara and Blake E Dewey and Matthew K Schindler and John Muschelli and Daniel S Reich and Ciprian M Crainiceanu and Ani Eloyan},
  journal = {NeuroImage: Clinical},
  volume = {10},
  pages = {1--17},
  year = {2016},
  publisher = {Elsevier},
}

@Article{muschelli2015validated,
  title = {Validated automatic brain extraction of head {CT} images},
  author = {John Muschelli and Natalie L Ullman and W Andrew Mould and Paul Vespa and Daniel F Hanley and Ciprian M Crainiceanu},
  journal = {NeuroImage},
  volume = {114},
  pages = {379--385},
  year = {2015},
  publisher = {Academic Press},
}

@Article{muschelli2015fslr,
  title = {{fslr}: Connecting the {FSL} Software with {R}},
  author = {John Muschelli and Elizabeth Sweeney and Martin Lindquist and Ciprian Crainiceanu},
  journal = {R Journal},
  volume = {7},
  number = {1},
  pages = {163--175},
  year = {2015},
  publisher = {R Foundation for Statistical Computing},
}

@Article{muschelli2015quantitative,
  title = {Quantitative Intracerebral Hemorrhage Localization},
  author = {John Muschelli and Natalie L Ullman and Elizabeth M Sweeney and Ani Eloyan and Neil Martin and Paul Vespa and Daniel F Hanley and Ciprian M Crainiceanu},
  journal = {Stroke},
  volume = {46},
  number = {11},
  pages = {3270--3273},
  year = {2015},
  publisher = {Am Heart Assoc},
}

@Article{choe2015reproducibility,
  title = {Reproducibility and temporal structure in weekly resting-state {fMRI} over a period of 3.5 years},
  author = {Ann S Choe and Craig K Jones and Suresh E Joel and John Muschelli and Visar Belegu and Brian S Caffo and Martin A Lindquist and Peter CM {van Zijl} and James J Pekar},
  journal = {PloS one},
  volume = {10},
  number = {10},
  pages = {e0140134},
  year = {2015},
  publisher = {Public Library of Science},
}

@Article{webb2015accuracy,
  title = {Accuracy of the {ABC}/2 Score for Intracerebral Hemorrhage Systematic Review and Analysis of {MISTIE}, {CLEAR-IVH}, and {CLEAR III}},
  author = {Alastair JS Webb and Natalie L Ullman and Tim C Morgan and John Muschelli and Joshua Kornbluth and Issam A Awad and Stephen Mayo and Michael Rosenblum and Wendy Ziai and {Aldrich} and Francois Mario Zuccarrello and Sayona John and Sagi Harnof and George Lopez and William C. Broaddus and Christine Wijman and Paul Vespa and Ross Bullock and Stephen J. Haines and Salvador Cruz-Flores and Stan Tuhrim and Michael D. Hill and Raj Narayan and Daniel F. Hanley},
  journal = {Stroke},
  volume = {46},
  number = {9},
  pages = {2470--2476},
  year = {2015},
  publisher = {Am Heart Assoc},
}

@Article{muschelli2014brainr,
  title = {{brainR}: Interactive 3 and {4D} Images of High Resolution Neuroimage Data},
  author = {John Muschelli and Elizabeth Sweeney and Ciprian Crainiceanu},
  journal = {R Journal},
  volume = {6},
  number = {1},
  pages = {41--48},
  year = {2014},
}

@Article{muschelli2014reduction,
  title = {Reduction of motion-related artifacts in resting state {fMRI} using {aCompCor}},
  author = {John Muschelli* and Mary Beth Nebel* and Brian S Caffo and Anita D Barber and James J Pekar and Stewart H Mostofsky},
  journal = {NeuroImage},
  volume = {96},
  pages = {22--35},
  year = {2014},
  publisher = {Academic Press},
}

@Article{eloyan2014analytic,
  title = {Analytic programming with {fMRI} data: A quick-start guide for statisticians using {R}},
  author = {Ani Eloyan and Shanshan Li and John Muschelli and Jim J Pekar and Stewart H Mostofsky and Brian S Caffo},
  journal = {PLOS ONE},
  volume = {9},
  number = {2},
  pages = {e89470},
  year = {2014},
}

@Article{nebel2014disruption,
  title = {Disruption of functional organization within the primary motor cortex in children with autism},
  author = {Mary Beth Nebel and Suresh E Joel and John Muschelli and Anita D Barber and Brian S Caffo and James J Pekar and Stewart H Mostofsky},
  journal = {Human Brain Mapping},
  volume = {35},
  number = {2},
  pages = {567--580},
  year = {2014},
}

@Article{mould2013minimally,
  title = {Minimally invasive surgery plus recombinant tissue-type plasminogen activator for intracerebral hemorrhage evacuation decreases perihematomal edema},
  author = {W Andrew Mould and J Ricardo Carhuapoma and John Muschelli and Karen Lane and Timothy C Morgan and Nichol A McBee and Amanda J Bistran-Hall and Natalie L Ullman and Paul Vespa and Neil A Martin and Issam Awad and Mario Zuccarello and Daniel F. Hanley},
  journal = {Stroke},
  volume = {44},
  number = {3},
  pages = {627--634},
  year = {2013},
  publisher = {Lippincott Williams \& Wilkins},
}

@Article{mould2013mistie,
  title = {{MISTIE} Investigators: minimally invasive surgery plus recombinant tissue-type plasminogen activator for intracerebral hemorrhage evacuation decreases perihematomal edema},
  author = {WA Mould and JR Carhuapoma and J Muschelli and K Lane and TC Morgan and NA McBee and AJ Bistran-Hall and NL Ullman and P Vespa and NA Martin and Issam Awad and Mario Zuccarello and Daniel F. Hanley},
  journal = {Stroke},
  volume = {44},
  number = {3},
  pages = {627--634},
  year = {2013},
}

@Article{bundy2012ambulatory,
  title = {Ambulatory care connections of medicaid-insured children with sickle cell disease},
  author = {David G Bundy and John Muschelli and Gwendolyn D Clemens and John J Strouse and Richard E Thompson and James F Casella and Marlene R Miller},
  journal = {Pediatric Blood \& Cancer},
  year = {2012},
  volume = {59},
  number = {5},
  pages = {888--894},
  publisher = {Wiley Online Library},
}

@Article{eloyan2012automated,
  title = {Automated diagnoses of attention deficit hyperactive disorder using magnetic resonance imaging},
  author = {Ani Eloyan and John Muschelli and Mary Beth Nebel and Han Liu and Fang Han and Tuo Zhao and Anita D Barber and Suresh Joel and James J Pekar and Stewart H Mostofsky and others},
  journal = {Frontiers in Systems Neuroscience},
  volume = {6},
  year = {2012},
  pages = {6},
  publisher = {Frontiers Media SA},
}

@Article{hinson2012drainage,
  title = {Drainage efficiency with dual versus single catheters in severe intraventricular hemorrhage},
  author = {Holly E Hinson and Eric Melnychuk and John Muschelli and Daniel F Hanley and Issam A Awad and Wendy C Ziai},
  journal = {Neurocritical Care},
  volume = {16},
  number = {3},
  pages = {399--405},
  year = {2012},
  publisher = {Humana Press Inc},
}

@Article{jaffe2012ventricular,
  title = {Ventricular catheter location and the clearance of intraventricular hemorrhage},
  author = {Jennifer Jaffe and Eric Melnychuk and John Muschelli and Wendy Ziai and Timothy Morgan and Daniel F Hanley and Issam A Awad},
  journal = {Neurosurgery},
  volume = {70},
  number = {5},
  pages = {1258--1264},
  year = {2012},
  publisher = {NIH Public Access},
}

@Article{webb2012resolution,
  title = {Resolution of Intraventricular Hemorrhage Varies by Ventricular Region and Dose of Intraventricular Thrombolytic The Clot Lysis: Evaluating Accelerated Resolution of {IVH} ({CLEAR} {IVH}) Program},
  author = {Alastair JS Webb and Natalie L Ullman and Sarah Mann and John Muschelli and Issam A Awad and Daniel F Hanley},
  journal = {Stroke},
  volume = {43},
  number = {6},
  pages = {1666--1668},
  year = {2012},
  publisher = {Lippincott Williams \& Wilkins},
}

@Article{ziai2012factors,
  title = {Factors affecting clot lysis rates in patients with spontaneous intraventricular hemorrhage},
  author = {Wendy C Ziai and John Muschelli and Carol B Thompson and Penelope M Keyl and Karen Lane and Shuai Shao and Daniel F Hanley},
  journal = {Stroke},
  volume = {43},
  number = {5},
  pages = {1234--1239},
  year = {2012},
  publisher = {Lippincott Williams \& Wilkins},
}

@Article{newell2011minimally,
  title = {Minimally invasive evacuation of spontaneous intracerebral hemorrhage using sonothrombolysis},
  author = {David W Newell and M Mohsin Shah and Robert Wilcox and Douglas R Hansmann and Erik Melnychuk and John Muschelli and Daniel F Hanley},
  journal = {Journal of Neurosurgery},
  volume = {115},
  number = {3},
  pages = {592--601},
  year = {2011},
  publisher = {NIH Public Access},
}

@Article{niedner2011epidemiology,
  title = {Epidemiology of central line-associated bloodstream infections in the pediatric intensive care unit},
  author = {Matthew F Niedner and W Charles Huskins and Elizabeth Colantuoni and John Muschelli and J Mitchell Harris and Tom B Rice and Richard J Brilli and Marlene R Miller},
  journal = {Infection Control},
  volume = {32},
  number = {12},
  pages = {1200--1208},
  year = {2011},
  publisher = {Cambridge University Press},
}