Artificial intelligence for dementia genetics and omics

C. Bettencourt, Nathan G. Skene, S. Bandres-Ciga, Emma Anderson, L. Winchester, I. Foote, Jeremy Schwartzentruber, J. Botía, M. Nalls, A. Singleton, B. Schilder, J. Humphrey, Sarah J. Marzi, Christina E. Toomey, Ahmad Al Kleifat, E. Harshfield, V. Garfield, C. Sandor, Samuel Keat, S. Tamburin, C. S. Frigerio, I. Lourida, J. Ranson, D. Llewellyn

Alzheimer's & Dementia, 2023

Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology

O. Ziff, Jacob Neeves, Jamie S. Mitchell, Giulia E. Tyzack, C. Martínez-Ruiz, Raphaëlle Luisier, A. Chakrabarti, N. Mcgranahan, K. Litchfield, S. Boulton, A. Al-Chalabi, Gavin P. Kelly, J. Humphrey, R. Patani

Nature Communications, 2023

Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing

Jack Humphrey, Erica Brophy, R. Kosoy, Biao Zeng, Elena Coccia, Daniele Mattei, Ashvin Ravi, Anastasia G. Efthymiou, Elisa Navarro, Benjamin Z Muller, G. J. Snijders, Amanda Allan, Alexandra Münch, Reta Birhanu Kitata, S. Kleopoulos, S. Argyriou, Z. Shao, Nancy Francoeur, Chia-Feng Tsai, Marina A. Gritsenko, M. Monroe, V. Paurus, K. Weitz, Tujin Shi, R. Sebra, Tao Liu, L. D. de Witte, A. Goate, D. Bennett, V. Haroutunian, G. Hoffman, J. Fullard, P. Roussos, Towfique Raj

medRxiv, 2023

Genetic analysis of the human microglia transcriptome across brain regions, aging and disease pathologies

Katia de Paiva Lopes, G. Snijders, J. Humphrey, Amanda Allan, M. Sneeboer, Elisa Navarro, B. Schilder, R. Vialle, M. Parks, Roy Missall, Welmoed van Zuiden, F. Gigase, Raphael Kübler, Amber Berdenis van Berlekom, Emily M. Hicks, Chotima Bӧttcher, J. Priller, R. Kahn, L. D. de Witte, T. Raj

Nature Genetics, 2022

Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes

J. Humphrey, S. Venkatesh, R. Hasan, Jake T. Herb, K. de Paiva Lopes, Fahri Küçükali, M. Byrska-Bishop, U. S. Evani, G. Narzisi, D. Fagegaltier, K. Sleegers, H. Phatnani, David A. Knowles, P. Fratta, T. Raj

Nature Neuroscience, 2022

TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A

Anna L. Brown, O. Wilkins, M. Keuss, Sarah E. Hill, M. Zanovello, Weaverly Colleen Lee, A. Bampton, Flora C. Y. Lee, L. Masino, Y. Qi, S. Bryce-Smith, A. Gatt, Martina Hallegger, D. Fagegaltier, H. Phatnani, Hemali Justin Dhruv James R. Zachary Ximena Edward B. Viv Phatnani Kwan Sareen Broach Simmons Arcila-Londono, Justin Kwan, D. Sareen, James R. Broach, Zachary Simmons, X. Arcila-Londono, Edward B. Lee, V. V. Van Deerlin, N. Shneider, E. Fraenkel, L. Ostrow, Frank Baas, Noah Zaitlen, James D. Berry, A. Malaspina, P. Fratta, Gregory A. Cox, Leslie M. Thompson, Steve Finkbeiner, E. Dardiotis, Timothy Miller, Siddharthan Chandran, S. Pal, E. Hornstein, D. Macgowan, Terry Heiman-Patterson, M. G. Hammell, N. Patsopoulos, O. Butovsky, Joshua Dubnau, Avindra Nath, Robert Bowser, Matthew M Harms, Eleonora Aronica, Mary Poss, Jennifer Phillips-Cremins, John Crary, N. Atassi, Dale J. Lange, Darius J. Adams, Leonidas Stefanis, M. Gotkine, Robert H. Baloh, Suma Babu, Towfique Raj, S. Paganoni, Ophir Shalem, Colin Smith, Bin Zhang, Brent Harris, Iris J. Broce, V. Drory, J. Ravits, Corey McMillan, Vilas Menon, Lani Wu, Steve Altschuler, Y. Lerner, Rita Sattler, K. Van Keuren-Jensen, O. Rozenblatt-Rosen, Kerstin Lindblad-Toh, Katharine Nicholson, Peter Gregersen, Jeong H. Lee, Sulev Kokos, Stephen Muljo, J. Newcombe, E. Gustavsson, S. Seddighi, Joel F Reyes, Steve Coon, Daniel M. Ramos, G. Schiavo, E.M.C. Fisher, Towfique Raj, M. Secrier, T. Lashley, J. Ule, E. Buratti, J. Humphrey, Michael E. Ward, P. Fratta

Nature, 2022

Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions

Rahat Hasan, J. Humphrey, C. Bettencourt, J. Newcombe, T. Lashley, P. Fratta, T. Raj

Acta Neuropathologica, 2021

FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention

J. Humphrey, N. Birsa, Carmelo Milioto, Martha McLaughlin, A. Ule, D. Robaldo, A. B. Eberle, Rahel Kräuchi, Matthew Bentham, Anna L. Brown, Seth Jarvis, C. Bodo, M. G. Garone, A. Devoy, G. Soraru', A. Rosa, I. Bozzoni, E. Fisher, O. Mühlemann, G. Schiavo, M. Ruepp, A. Isaacs, V. Plagnol, P. Fratta

Nucleic Acids Research, 2020

Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia.

M. Prudencio, J. Humphrey, Sarah R Pickles, Anna L. Brown, Sarah E. Hill, J. Kachergus, Ji Shi, M. Heckman, Matthew R. Spiegel, C. Cook, Yuping Song, Mei Yue, Lillian M. Daughrity, Y. Carlomagno, Karen R. Jansen-West, Cristhoper H. Fernandez De Castro, M. DeTure, S. Koga, Ying-Chih Wang, P. Sivakumar, C. Bodo, A. Candalija, K. Talbot, B. Selvaraj, K. Burr, S. Chandran, J. Newcombe, T. Lashley, I. Hubbard, Demetra Catalano, Duyang Kim, Nadia A. Propp, S. Fennessey, D. Fagegaltier, H. Phatnani, M. Secrier, E. Fisher, B. Oskarsson, M. van Blitterswijk, R. Rademakers, N. Graff-Radford, B. Boeve, D. Knopman, R. Petersen, K. Josephs, E. Thompson, T. Raj, Michael E. Ward, Dennis W. Dickson, T. Gendron, P. Fratta, L. Petrucelli

Journal of Clinical Investigation, 2020

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

T. Raj, Yang I. Li, G. Wong, J. Humphrey, Minghui Wang, Satesh Ramdhani, Ying-Chih Wang, B. Ng, Ishaan Gupta, V. Haroutunian, E. Schadt, Tracy L. Young-Pearse, S. Mostafavi, Bin Zhang, P. Sklar, D. Bennett, P. D. De Jager

Nature Genetics, 2018

Mice with endogenous TDP‐43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis

P. Fratta, P. Sivakumar, J. Humphrey, K. Lo, T. Ricketts, H. Oliveira, J. M. Brito-Armas, B. Kalmar, A. Ule, Yichao Yu, N. Birsa, C. Bodo, T. Collins, Alexander E. Conicella, Alan Mejia Maza, A. Marrero-Gagliardi, M. Stewart, J. Mianné, Silvia Corrochano, W. Emmett, G. Codner, M. Groves, R. Fukumura, Y. Gondo, M. Lythgoe, E. Pauws, E. Peskett, P. Stanier, L. Teboul, Martina Hallegger, A. Calvo, A. Chiò, A. Isaacs, N. Fawzi, Eric T. Wang, D. Housman, F. Baralle, L. Greensmith, E. Buratti, V. Plagnol, E. Fisher, A. Acevedo-Arozena

EMBO Journal, 2018

Annotation-free quantification of RNA splicing using LeafCutter

Yang I. Li, David A. Knowles, J. Humphrey, A. Barbeira, Scott P. Dickinson, H. Im, J. Pritchard

Nature Genetics, 2017

Humanized mutant FUS drives progressive motor neuron degeneration without aggregation in ‘FUSDelta14’ knockin mice

A. Devoy, B. Kalmar, M. Stewart, H. Park, B. Burke, Suzanna Noy, Yushi T. Redhead, J. Humphrey, K. Lo, J. Jaeger, Alan Mejia Maza, P. Sivakumar, C. Bertolin, G. Soraru', V. Plagnol, L. Greensmith, Abraham Acevedo Arozena, A. Isaacs, B. Davies, P. Fratta, E. Fisher

Brain : a journal of neurology, 2017

Quantitative analysis of cryptic splicing associated with TDP-43 depletion

J. Humphrey, W. Emmett, P. Fratta, A. Isaacs, V. Plagnol

BMC Medical Genomics, 2016