Selected Publications

Peter A. Wijeratne, Arman Eshaghi, William J. Scotton, Maitrei Kohli, Leon Aksman, Neil P. Oxtoby, Dorian Pustina, John H. Warner, Jane S. Paulsen, Rachael I. Scahill, Cristina Sampaio, Sarah J. Tabrizi, Daniel C. Alexander (2023). The temporal event-based model: Learning event timelines in progressive diseases. Imaging Neuroscience.

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PA Wijeratne, DC Alexander (2021). Learning Transition Times in Event Sequences: The Temporal Event-Based Model of Disease Progression.

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Jacob W. Vogel, Alexandra L. Young, Neil P. Oxtoby, Ruben Smith, Rik Ossenkoppele, Olof T. Strandberg, Renaud La Joie, Leon M. Aksman, Michel J. Grothe, Yasser Iturria-Medina, the Alzheimer’s Disease Neuroimaging Initiative, Michael J. Pontecorvo, Michael D. Devous, Gil D. Rabinovici, Daniel C. Alexander, Chul Hyoung Lyoo, Alan C. Evans, Oskar Hansson (2021). Four distinct trajectories of tau deposition identified in Alzheimer’s disease. Nature Medicine.

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Arman Eshaghi, Alexandra L. Young, Peter A. Wijeratne, Ferran Prados, Douglas L. Arnold, Sridar Narayanan, Charles R. G. Guttmann, Frederik Barkhof, Daniel C. Alexander, Alan J. Thompson, Declan Chard, Olga Ciccarelli (2021). Identifying multiple sclerosis subtypes using unsupervised machine learning and MRI data. Nature Communications.

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N Oxtoby, L Leyland, L Aksman, G Thomas, E Bunting, P Wijeratne, A Young, A Zarkali, M Tan, F Bremner, P Keane, H Morris, A Schrag, D Alexander, R Weil (2021). Sequence of clinical and neurodegeneration events in Parkinson's disease progression. Brain: a journal of Neurology.

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(2021). The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up. Machine Learning for Biomedical Imaging.

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Leon M. Aksman, Peter A. Wijeratne, Neil P. Oxtoby, Arman Eshaghi, Cameron Shand, Andre Altmann, Daniel C. Alexander, Alexandra L. Young (2021). pySuStaIn: A Python implementation of the Subtype and Stage Inference algorithm. SoftwareX.

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Alexandra L. Young, Jacob W. Vogel, Leon M. Aksman, Peter A. Wijeratne, Arman Eshaghi, Neil P. Oxtoby, Steven C. R. Williams, Daniel C. Alexander, for the Alzheimer’s Disease Neuroimaging Initiative (2021). Ordinal SuStaIn: Subtype and Stage Inference for Clinical Scores, Visual Ratings, and Other Ordinal Data. Frontiers in Artificial Intelligence.

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Damiano Archetti, Alexandra L. Young, Neil P. Oxtoby, Daniel Ferreira, Gustav Mårtensson, Eric Westman, Daniel C. Alexander, Giovanni B. Frisoni, Alberto Redolfi, for Alzheimer’s Disease Neuroimaging Initiative , EuroPOND Consortium (2021). Inter-Cohort Validation of SuStaIn Model for Alzheimer’s Disease. Frontiers in Big Data.

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M Bellio, NP Oxtoby, Z Walker, S Henley, A Ribbens, A Blandford, DC Alexander, KXX Yong (2020). Analyzing large Alzheimer's disease cognitive datasets: Considerations and challenges. Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring.

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PA Wijeratne, DC Alexander (2020). Learning transition times in event sequences: the Event-Based Hidden Markov Model of disease progression.

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A O'Connor, PSJ Weston, IM Pavisic, NS Ryan, JD Collins, K Lu, SJ Crutch, DC Alexander, NC Fox, NP Oxtoby (2020). Quantitative detection and staging of presymptomatic cognitive decline in familial Alzheimer's disease: a retrospective cohort analysis. ALZHEIMERS RESEARCH & THERAPY.

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R Pascuzzo, NP Oxtoby, AL Young, J Blevins, G Castelli, S Garbarino, ML Cohen, LB Schonberger, P Gambetti, BS Appleby, DC Alexander, A Bizzi (2020). Prion propagation estimated from brain diffusion MRI is subtype dependent in sporadic Creutzfeldt–Jakob disease. Acta Neuropathologica.

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SM Sisodiya, CD Whelan, SN Hatton, K Huynh, A Altmann, M Ryten, A Vezzani, ME Caligiuri, A Labate, A Gambardella, V Ives-Deliperi, S Meletti, BC Munsell, L Bonilha, M Tondelli, M Rebsamen, C Rummel, AE Vaudano, R Wiest, AR Balachandra, N Bargalló, E Bartolini, A Bernasconi, N Bernasconi, B Bernhardt, B Caldairou, SJA Carr, GL Cavalleri, F Cendes, L Concha, PM Desmond, M Domin, JS Duncan, NK Focke, R Guerrini, K Hamandi, GD Jackson, N Jahanshad, R Kälviäinen, SS Keller, P Kochunov, MA Kowalczyk, BAK Kreilkamp, P Kwan, S Lariviere, M Lenge, SM Lopez, P Martin, M Mascalchi, JCV Moreira, ME Morita-Sherman, HR Pardoe, JC Pariente, K Raviteja, CS Rocha, R Rodríguez-Cruces, M Seeck, MKHG Semmelroch, B Sinclair, H Soltanian-Zadeh, DJ Stein, P Striano, PN Taylor, RH Thomas, SI Thomopoulos, D Velakoulis, L Vivash, B Weber, CL Yasuda, J Zhang, PM Thompson, CR McDonald (2020). The ENIGMA-Epilepsy working group: Mapping disease from large data sets. Human Brain Mapping.

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PA Wijeratne, EB Johnson, A Eshaghi, L Aksman, S Gregory, HJ Johnson, GR Poudel, A Mohan, C Sampaio, N Georgiou-Karistianis, JS Paulsen, SJ Tabrizi, RI Scahill, PREDICT-HD, IMAGE-HD, TRACK-HD investigators, DC Alexander (2020). Robust markers and sample sizes for multi-centre trials of Huntington's disease.. Ann Neurol.

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FM Aarestrup, A Albeyatti, WJ Armitage, C Auffray, L Augello, R Balling, N Benhabiles, G Bertolini, JG Bjaalie, M Black, others (2020). Towards a European Health Research and Innovation Cloud (HRIC). Genome medicine.

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Nicholas C. Firth, Silvia Primativo, Emilie Brotherhood, Alexandra L. Young, Keir X.X. Yong, Sebastian J. Crutch, Daniel C. Alexander, Neil P. Oxtoby (2020). Sequences of cognitive decline in typical Alzheimer's disease and posterior cortical atrophy estimated using a novel event-based model of disease progression. Alzheimer’s & Dementia.

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A Mihalik, M Brudfors, M Robu, FS Ferreira, H Lin, A Rau, T Wu, SB Blumberg, B Kanber, M Tariq, MDME Garcia, C Zor, DI Nikitichev, J Mourao-Miranda, NP Oxtoby (2019). ABCD Neurocognitive Prediction Challenge 2019: Predicting individual fluid intelligence scores from structural MRI using probabilistic segmentation and kernel ridge regression. **.

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Alexandra L. Young, Razvan V. Marinescu, Neil P. Oxtoby, Martina Bocchetta, Keir Yong, Nicholas C. Firth, David M. Cash, David L. Thomas, Katrina M. Dick, Jorge Cardoso, John van Swieten, Barbara Borroni, Daniela Galimberti, Mario Masellis, Maria Carmela Tartaglia, James B. Rowe, Caroline Graff, Fabrizio Tagliavini, Giovanni B Frisoni, Robert Laforce, Elizabeth Finger, Alexandre de Mendonça, Sandro Sorbi, Jason D. Warren, Sebastian Crutch, Nick C. Fox, Sebastien Ourselin, Jonathan M. Schott, Jonathan D. Rohrer, Daniel C. Alexander, Christin Andersson, Silvana Archetti, Andrea Arighi, Luisa Benussi, Giuliano Binetti, Sandra Black, Maura Cosseddu, Marie Fallström, Carlos Ferreira, Chiara Fenoglio, Morris Freedman, Giorgio G. Fumagalli, Stefano Gazzina, Roberta Ghidoni, Marina Grisoli, Vesna Jelic, Lize Jiskoot, Ron Keren, Gemma Lombardi, Carolina Maruta, Lieke Meeter, Simon Mead, Rick van Minkelen, Benedetta Nacmias, Linn Öijerstedt, Alessandro Padovani, Jessica Panman, Michela Pievani, Cristina Polito, Enrico Premi, Sara Prioni, Rosa Rademakers, Veronica Redaelli, Ekaterina Rogaeva, Giacomina Rossi, Martin Rossor, Elio Scarpini, David Tang-Wai, Hakan Thonberg, Pietro Tiraboschi, Ana Verdelho, Michael W. Weiner, Paul Aisen, Ronald Petersen, Clifford R. Jack, William Jagust, John Q. Trojanowki, Arthur W. Toga, Laurel Beckett, Robert C. Green, Andrew J. Saykin, John Morris, Leslie M. Shaw, Zaven Khachaturian, Greg Sorensen, Lew Kuller, Marc Raichle, Steven Paul, Peter Davies, Howard Fillit, Franz Hefti, Davie Holtzman, M. Marcel Mesulam, William Potter, Peter Snyder, Adam Schwartz, Tom Montine, Ronald G. Thomas, Michael Donohue, Sarah Walter, Devon Gessert, Tamie Sather, Gus Jiminez, Danielle Harvey, Matthew Bernstein, Paul Thompson, Norbert Schuff, Bret Borowski, Jeff Gunter, Matt Senjem, Prashanthi Vemuri, David Jones, Kejal Kantarci, Chad Ward, Robert A. Koeppe, Norm Foster, Eric M. Reiman, Kewei Chen, Chet Mathis, Susan Landau, Nigel J. Cairns, Erin Householder, Lisa Taylor-Reinwald, Virginia Lee, Magdalena Korecka, Michal Figurski, Karen Crawford, Scott Neu, Tatiana M. Foroud, Steven Potkin, Li Shen, Kelley Faber, Sungeun Kim, Kwangsik Nho, Leon Thal, Neil Buckholtz, Marylyn Albert, Richard Frank, John Hsiao, Jeffrey Kaye, Joseph Quinn, Betty Lind, Raina Carter, Sara Dolen, Lon S. Schneider, Sonia Pawluczyk, Mauricio Beccera, Liberty Teodoro, Bryan M. Spann, James Brewer, Helen Vanderswag, Adam Fleisher, Judith L. Heidebrink, Joanne L. Lord, Sara S. Mason, Colleen S. Albers, David Knopman, Kris Johnson, Rachelle S. Doody, Javier Villanueva-Meyer, Munir Chowdhury, Susan Rountree, Mimi Dang, Yaakov Stern, Lawrence S. Honig, Karen L. Bell, Beau Ances, Maria Carroll, Sue Leon, Mark A. Mintun, Stacy Schneider, Angela Oliver, Daniel Marson, Randall Griffith, David Clark, David Geldmacher, John Brockington, Erik Roberson, Hillel Grossman, Effie Mitsis, Leyla de Toledo-Morrell, Raj C. Shah, Ranjan Duara, Daniel Varon, Maria T. Greig, Peggy Roberts, Marilyn Albert, Chiadi Onyike, Daniel D'Agostino, Stephanie Kielb, James E. Galvin, Brittany Cerbone, Christina A. Michel, Henry Rusinek, Mony J. de Leon, Lidia Glodzik, Susan De Santi, P. Murali Doraiswamy, Jeffrey R. Petrella, Terence Z. Wong, Steven E. Arnold, Jason H. Karlawish, David Wolk, Charles D. Smith, Greg Jicha, Peter Hardy, Partha Sinha, Elizabeth Oates, Gary Conrad, Oscar L. Lopez, MaryAnn Oakley, Donna M. Simpson, Anton P. Porsteinsson, Bonnie S. Goldstein, Kim Martin, Kelly M. Makino, M. Saleem Ismail, Connie Brand, Ruth A. Mulnard, Gaby Thai, Catherine Mc-Adams-Ortiz, Kyle Womack, Dana Mathews, Mary Quiceno, Ramon Diaz-Arrastia, Richard King, Myron Weiner, Kristen Martin-Cook, Michael DeVous, Allan I. Levey, James J. Lah, Janet S. Cellar, Jeffrey M. Burns, Heather S. Anderson, Russell H. Swerdlow, Liana Apostolova, Kathleen Tingus, Ellen Woo, Daniel Hs Silverman, Po H. Lu, George Bartzokis, Neill R. Graff-Radford, Francine Parfitt, Tracy Kendall, Heather Johnson, Martin R. Farlow, Ann Marie Hake, Brandy R. Matthews, Scott Herring, Cynthia Hunt, Christopher H. van Dyck, Richard E. Carson, Martha G. MacAvoy, Howard Chertkow, Howard Bergman, Chris Hosein, Bojana Stefanovic, Curtis Caldwell, Ging-Yuek Robin Hsiung, Howard Feldman, Benita Mudge, Michele Assaly, Andrew Kertesz, John Rogers, Charles Bernick, Donna Munic, Diana Kerwin, Marek-Marsel Mesulam, Kristine Lipowski, Chuang-Kuo Wu, Nancy Johnson, Carl Sadowsky, Walter Martinez, Teresa Villena, Raymond Scott Turner, Kathleen Johnson, Brigid Reynolds, Reisa A. Sperling, Keith A. Johnson, Gad Marshall, Meghan Frey, Barton Lane, Allyson Rosen, Jared Tinklenberg, Marwan N. Sabbagh, Christine M. Belden, Sandra A. Jacobson, Sherye A. Sirrel, Neil Kowall, Ronald Killiany, Andrew E. Budson, Alexander Norbash, Patricia Lynn Johnson, Joanne Allard, Alan Lerner, Paula Ogrocki, Leon Hudson, Evan Fletcher, The Genetic FTD Initiative (GENFI), The Alzheimer's Disease Neuroimaging Initiative (ADNI) (2018). Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference. Nature Communications.

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PA Wijeratne, AL Young, NP Oxtoby, RV Marinescu, NC Firth, EB Johnson, A Mohan, C Sampaio, RI Scahill, SJ Tabrizi, DC Alexander (2018). An image-based model of brain volume biomarker changes in Huntington's disease. Annals of Clinical and Translational Neurology.

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Neil P Oxtoby, Alexandra L Young, David M Cash, Tammie L S Benzinger, Anne M Fagan, John C Morris, Randall J Bateman, Nick C Fox, Jonathan M Schott, Daniel C Alexander (2018). Data-driven models of dominantly-inherited Alzheimer's disease progression. Brain.

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Alexandra L. Young, Neil P. Oxtoby, Pankaj Daga, David M. Cash, Nick C. Fox, Sebastien Ourselin, Jonathan M. Schott, Daniel C., on behalf of the Alzheimer's Disease Neuroimaging Initiative Alexander (2014). A data-driven model of biomarker changes in sporadic Alzheimer's disease. Brain.

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